GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_04042 in Lactobacillus silagei IWT126

Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate WP_089137183.1 CES79_RS10735 amino acid permease

Query= uniprot:A0A2Z5MFR8
         (461 letters)



>NCBI__GCF_002217945.1:WP_089137183.1
          Length = 462

 Score =  330 bits (845), Expect = 8e-95
 Identities = 176/448 (39%), Positives = 276/448 (61%), Gaps = 8/448 (1%)

Query: 10  LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGEMV 69
           L+R +    +++I+LGGAIG GLF+GS S ++  GPS++L Y   G+I +++MR LGEM+
Sbjct: 11  LRRSMTAGQMEMISLGGAIGVGLFMGSTSTIKWTGPSVLLAYMFVGLILYIVMRALGEMI 70

Query: 70  AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTWVS 129
              P  GSF+ +A +Y     G+L+ W     Y++V M+E+ A   Y+ YWWP + T+  
Sbjct: 71  YVNPGTGSFADYATEYVHPLAGYLAKWANVFEYIVVGMSEVVAATQYLQYWWPHINTFTV 130

Query: 130 ALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSG--HGGPQASISN 187
            ++  A + A NLA+ KAYG  EFWFA+IKV+ +I MI+ G  ++  G  +GG     SN
Sbjct: 131 GVIIIAFLVAANLASAKAYGSLEFWFAMIKVITIIMMIILGLLVIFFGLGNGGHPVGFSN 190

Query: 188 LWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRILIF 247
           LWSHGGFF  G  G F  +++I+ S+ G+EL+GITA E   PQK+I K+V  V++RILIF
Sbjct: 191 LWSHGGFFTGGVKGFFFSMSIIVGSYEGIELLGITAGEVANPQKAIVKSVKSVLFRILIF 250

Query: 248 YICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVYANS 307
           Y+ ++ V++++YPWN ++A GSPFV  F+++G T  A+V+N VVLTAALS  NSG+Y++S
Sbjct: 251 YVGAIFVIVTIYPWNRLSAIGSPFVSTFAKVGITAAASVINFVVLTAALSSANSGIYSSS 310

Query: 308 RMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPA--EALGLLMALV 365
           RML+ LA + +AP+   ++ +R VP  AI   +   F   +++ +  A  ++   L  +V
Sbjct: 311 RMLFKLAHESDAPKIFGRLSKRVVPDAAILGISSGIFLGFLLDIIFSAYNKSTSDLFVVV 370

Query: 366 VAALVL----NWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILAM 421
            ++ VL     W +I L  L+ R+      +   FK   +P SN+  +  + +I+  + +
Sbjct: 371 FSSSVLPGMIPWFVILLAELRFRKNNAIVMKDHPFKLPLYPFSNYFAMFVLVVIVGFMFV 430

Query: 422 TPGLSVSVLLVPLWLVVMWAGYAFKRRR 449
            P   VSV++    LVV    Y  + R+
Sbjct: 431 NPDTRVSVIVGAAVLVVATLFYVVRHRK 458


Lambda     K      H
   0.327    0.140    0.440 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 505
Number of extensions: 29
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 461
Length of database: 462
Length adjustment: 33
Effective length of query: 428
Effective length of database: 429
Effective search space:   183612
Effective search space used:   183612
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory